Question: Galaxy cloud instance won't initialize
0
gravatar for ashamchu
4.0 years ago by
ashamchu10
Canada
ashamchu10 wrote:

Hi Galaxy Team,

 

I am in desperate need of using the cloud so that I can analyze by rather large RNAseq files.  I have followed all the steps to create an AWS account and initialize a cluster.

My computer keeps sticking at this point: "Initializing 'Galaxy' cluster type with storage type 'volume'. Please wait... (2014-12-05 00:52:55"  and the "Access Galaxy" button is still greyed out.

The Cluster Status Log is reading this:

  • 00:49:01 - Master starting
  • 00:49:03 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type.
  • 00:49:07 - Migration service prerequisites OK; starting the service
  • 00:49:07 - SGE service prerequisites OK; starting the service
  • 00:49:09 - Setting up SGE...
  • 00:49:54 - Empty disk usage for FS transient_nfs
  • 00:50:06 - Empty disk usage for FS transient_nfs
  • 00:50:19 - Empty disk usage for FS transient_nfs
  • 00:50:31 - Empty disk usage for FS transient_nfs
  • 00:50:43 - Empty disk usage for FS transient_nfs
  • 00:50:56 - Empty disk usage for FS transient_nfs
  • 00:51:08 - Empty disk usage for FS transient_nfs
  • 00:51:20 - Empty disk usage for FS transient_nfs
  • 00:51:33 - Empty disk usage for FS transient_nfs
  • 00:51:45 - Empty disk usage for FS transient_nfs
  • 00:51:57 - Empty disk usage for FS transient_nfs
  • 00:52:10 - Empty disk usage for FS transient_nfs
  • 00:52:22 - Empty disk usage for FS transient_nfs
  • 00:52:34 - Empty disk usage for FS transient_nfs
  • 00:52:47 - Empty disk usage for FS transient_nfs
  • 00:52:55 - Initializing 'Galaxy' cluster type with storage type 'volume'. Please wait...
  • 00:52:59 - Empty disk usage for FS transient_nfs
  • 00:52:59 - PostgreSQL data directory '/mnt/galaxy/db' does not exist (yet?)
  • 00:53:00 - Adding volume vol-17e28f0f (FS object for galaxy)...
  • 00:53:32 - Successfully grew file system FS object for galaxy
  • 00:53:32 - Successfully mounted file system /mnt/galaxy from /dev/xvdz
  • 00:53:35 - Adding volume vol-abe38eb3 (FS object for galaxyIndices)...
  • 00:53:40 - Attaching volume 'vol-abe38eb3' to instance 'i-a7201146' as device '/dev/sd{' failed. Exception: InvalidParameterValue (Value (/dev/sd{) for parameter device is invalid. /dev/sd{ is not a valid EBS device name.)
  • 00:53:40 - Postgres service prerequisites OK; starting the service
  • 00:53:50 - PostgreSQL daemon NOT running.
  • 00:53:50 - PostgreSQL daemon NOT running.
  • 00:53:54 - ProFTPd service prerequisites OK; starting the service
  • 00:54:00 - Empty disk usage for FS transient_nfs
  • 00:54:13 - Empty disk usage for FS transient_nfs
  • 00:54:13 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:54:26 - Empty disk usage for FS transient_nfs
  • 00:54:26 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:54:38 - Empty disk usage for FS transient_nfs
  • 00:54:39 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:54:51 - Empty disk usage for FS transient_nfs
  • 00:54:51 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:55:04 - Empty disk usage for FS transient_nfs
  • 00:55:04 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:55:17 - Empty disk usage for FS transient_nfs
  • 00:55:17 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:55:29 - Empty disk usage for FS transient_nfs
  • 00:55:29 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:55:42 - Empty disk usage for FS transient_nfs
  • 00:55:42 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:55:55 - Empty disk usage for FS transient_nfs
  • 00:55:55 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:56:07 - Empty disk usage for FS transient_nfs
  • 00:56:07 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:56:20 - Empty disk usage for FS transient_nfs
  • 00:56:20 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:56:33 - Empty disk usage for FS transient_nfs
  • 00:56:33 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:56:45 - Empty disk usage for FS transient_nfs
  • 00:56:46 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:56:58 - Empty disk usage for FS transient_nfs
  • 00:56:58 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:57:11 - Empty disk usage for FS transient_nfs
  • 00:57:11 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:57:23 - Empty disk usage for FS transient_nfs
  • 00:57:24 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:57:36 - Empty disk usage for FS transient_nfs
  • 00:57:36 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:57:49 - Empty disk usage for FS transient_nfs
  • 00:57:49 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:58:01 - Empty disk usage for FS transient_nfs
  • 00:58:02 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:58:14 - Empty disk usage for FS transient_nfs
  • 00:58:14 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:58:27 - Empty disk usage for FS transient_nfs
  • 00:58:27 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:58:39 - Empty disk usage for FS transient_nfs
  • 00:58:39 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:58:52 - Empty disk usage for FS transient_nfs
  • 00:58:52 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:59:05 - Empty disk usage for FS transient_nfs
  • 00:59:05 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:59:17 - Empty disk usage for FS transient_nfs
  • 00:59:17 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:59:30 - Empty disk usage for FS transient_nfs
  • 00:59:30 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:59:43 - Empty disk usage for FS transient_nfs
  • 00:59:43 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 00:59:55 - Empty disk usage for FS transient_nfs
  • 00:59:56 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:00:08 - Empty disk usage for FS transient_nfs
  • 01:00:08 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:00:21 - Empty disk usage for FS transient_nfs
  • 01:00:21 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:00:33 - Empty disk usage for FS transient_nfs
  • 01:00:34 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:00:46 - Empty disk usage for FS transient_nfs
  • 01:00:46 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:00:59 - Empty disk usage for FS transient_nfs
  • 01:00:59 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:01:11 - Empty disk usage for FS transient_nfs
  • 01:01:12 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:01:24 - Empty disk usage for FS transient_nfs
  • 01:01:24 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:01:37 - Empty disk usage for FS transient_nfs
  • 01:01:37 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:01:49 - Empty disk usage for FS transient_nfs
  • 01:01:50 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:02:02 - Empty disk usage for FS transient_nfs
  • 01:02:02 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:02:15 - Empty disk usage for FS transient_nfs
  • 01:02:15 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:02:28 - Empty disk usage for FS transient_nfs
  • 01:02:28 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:02:40 - Empty disk usage for FS transient_nfs
  • 01:02:40 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:02:53 - Empty disk usage for FS transient_nfs
  • 01:02:53 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:03:05 - Empty disk usage for FS transient_nfs
  • 01:03:06 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:03:18 - Empty disk usage for FS transient_nfs
  • 01:03:18 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:03:31 - Empty disk usage for FS transient_nfs
  • 01:03:31 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:03:44 - Empty disk usage for FS transient_nfs
  • 01:03:44 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:03:56 - Empty disk usage for FS transient_nfs
  • 01:03:57 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:04:09 - Empty disk usage for FS transient_nfs
  • 01:04:09 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:04:22 - Empty disk usage for FS transient_nfs
  • 01:04:22 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:04:34 - Empty disk usage for FS transient_nfs
  • 01:04:35 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:04:47 - Empty disk usage for FS transient_nfs
  • 01:04:47 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:05:00 - Empty disk usage for FS transient_nfs
  • 01:05:00 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:05:12 - Empty disk usage for FS transient_nfs
  • 01:05:13 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:05:25 - Empty disk usage for FS transient_nfs
  • 01:05:25 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:05:38 - Empty disk usage for FS transient_nfs
  • 01:05:38 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:05:50 - Empty disk usage for FS transient_nfs
  • 01:05:51 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:06:03 - Empty disk usage for FS transient_nfs
  • 01:06:03 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:06:16 - Empty disk usage for FS transient_nfs
  • 01:06:16 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:06:29 - Empty disk usage for FS transient_nfs
  • 01:06:29 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:06:41 - Empty disk usage for FS transient_nfs
  • 01:06:41 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:06:54 - Empty disk usage for FS transient_nfs
  • 01:06:54 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:07:07 - Empty disk usage for FS transient_nfs
  • 01:07:07 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:07:19 - Empty disk usage for FS transient_nfs
  • 01:07:19 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:07:32 - Empty disk usage for FS transient_nfs
  • 01:07:32 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:07:45 - Empty disk usage for FS transient_nfs
  • 01:07:45 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:07:57 - Empty disk usage for FS transient_nfs
  • 01:07:57 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:08:10 - Empty disk usage for FS transient_nfs
  • 01:08:10 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:08:23 - Empty disk usage for FS transient_nfs
  • 01:08:23 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:08:35 - Empty disk usage for FS transient_nfs
  • 01:08:36 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:08:48 - Empty disk usage for FS transient_nfs
  • 01:08:48 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0
  • 01:09:01 - Empty disk usage for FS transient_nfs
  • 01:09:01 - STATUS CHECK: File system named 'galaxyIndices' is not mounted. Error code 0

Any help/advice on how to get this working would be so greatly appreciated!  Thank you!

 

 

 

 

cloud indices • 1.1k views
ADD COMMENTlink modified 4.0 years ago by Dannon Baker3.7k • written 4.0 years ago by ashamchu10
0
gravatar for Dannon Baker
4.0 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

I see what happened here, but I'm not sure how (yet).  Can you provide a few more details from the primary cloudman log in the admin panel?  And, how did you launch this instance?  usegalaxy.org/cloudlaunch?  I just tested launching a new instance there and it seems to be working for me so far.

One hunch is that this might have been launched using an incompatible AMI, but that's just a guess without more information.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Dannon Baker3.7k
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